Genome-Wide DNA Methylation Profiling of Oesophageal Cancer-Associated Myofibroblasts
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ABSTRACT: The Illumina Infinium HumanMethylation450 BeadChip arrays were performed on a collection of primary oesophageal cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM). CAM and ATM samples were obtained from patients with oesophageal adenocarcinomas undergoing cancer surgery.
Project description:The Illumina Infinium HumanMethylation450 BeadChip arrays were performed on a collection of primary gastric cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM) as well as unrelated normal tissue myofibroblasts (NTM). CAM and ATM samples were obtained from patients undergoing gastric cancer surgery; whereas NTM samples were generated from deceased transplant donors with normal morphology.
Project description:The Illumina HumanHT-12v4 Expression BeadChip arrays were performed on a collection of primary gastric cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM) as well as unrelated normal tissue myofibroblasts (NTM). CAM and ATM samples were obtained from patients undergoing gastric cancer surgery; whereas NTM samples were generated from deceased transplant donors with normal morphology.
Project description:The Illumina HumanHT-12v4 Expression BeadChip arrays were performed on a collection of primary gastric cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM) as well as unrelated normal tissue myofibroblasts (NTM). CAM and ATM samples were obtained from patients undergoing gastric cancer surgery; whereas NTM samples were generated from deceased transplant donors with normal morphology.
Project description:We prepared miRNA from myofibroblats derived from normal oesophagus and esophageal cancers. miRCURYTM LNA Array ver5 was performed and comparisons were made by the dual (reference) method. Briefly, we have myofibroblast (NTM) from normal stomach and oesophagus, and we would like to establish whether there is tissue specific myofibroblast miRNA signature. Within the stomach (gastric) we made myofibroblasts from cancer (CAM) and adjacent tissue (ATM) from the same patients and myofibroblasts from healthy individuals (NTM) and we want to compare the matching ones paired and the total numbers unpaired. We have the same experimental design within the oesophagus but there we have two types of cancers (squamous and adenocarcinoma) so we wanted to do them separately for the two different groups and all together. In order to facilitate comparisons within each tissue type, we have used a different common reference for each tissue, and to compare between tissues using single colour analysis. Dual reference method was used to compare samples within a tissue and singe channel (quantile method) was used to compare samples across tissues.
Project description:Examination of DNA methylome patterns for potential subtypes in a larger cohort of ME/CFS samples using the Illumina Infinium HumanMethylation450 Beadchip Array Bisulfite-converted DNA from 25 samples were hybridised onto the Illumina Infinium HumanMethylation450 Beadchip Array
Project description:We present data from tissues of seven oesophageal adenocarcinomas of CD4 and CD8 T cell epitopes eluted from the cell surface using mass spectrometry (immunopeptidomics) of presented HLA bound peptides.This dataset forms part of the publication:Nicholas, B., Bailey, A., McCann, K.J., Wood, O., Walker, R.C., Parker, R., Ternette, N., Elliott, T., Underwood, T.J., Johnson, P. and Skipp, P. (2022), Identification of neoantigens in esophageal adenocarcinoma. Immunology. Accepted Author Manuscript. https://doi.org/10.1111/imm.13578
Project description:An Infinium microarray (Illumina HumanMethylation450 BeadChip) was used to generate DNA methylation data from human tissue samples.
Project description:DNA methylation profiling using Illumina Infinium HumanMethylation450 BeadChip arrays was used to assign cell lines to previously defined subgroups.